Add new class SpectrumList

DESCRIPTION

@@ -63,6 +63,7 @@ Depends:
     Biobase (>= 2.15.2),
     mzR (>= 2.15.1),
     BiocParallel,
+    S4Vectors,
     ProtGenerics (>= 1.9.1)
 Imports:
     IRanges (>= 2.13.28),
@@ -79,7 +80,6 @@ Imports:
     digest,
     lattice,
     ggplot2,
-    S4Vectors,
     XML,
     scales,
     MASS,
@@ -117,3 +117,95 @@ URL: https://github.com/lgatto/MSnbase
 biocViews: Infrastructure, Proteomics, MassSpectrometry,
     QualityControl, DataImport
 RoxygenNote: 6.1.0
+Collate: 
+    'AllClassUnions.R'
+    'AllGenerics.R'
+    'DataClasses.R'
+    'MzTab.R'
+    'NTR.R'
+    'RcppExports.R'
+    'SpectrumList.R'
+    'SpectrumList-methods.R'
+    'TMT10.R'
+    'TMT11.R'
+    'TMT6.R'
+    'TMT7.R'
+    'averageMSnSet.R'
+    'cache.R'
+    'coerce.R'
+    'combineFeatures.R'
+    'compfnames.R'
+    'environment.R'
+    'fData-utils.R'
+    'fdata-selection.R'
+    'foi.R'
+    'functions-Chromatogram.R'
+    'functions-Chromatograms.R'
+    'functions-MIAPE.R'
+    'functions-MSnExp.R'
+    'functions-MSnProcess.R'
+    'functions-MSnSet.R'
+    'functions-OnDiskMSnExp.R'
+    'functions-ReporterIons.R'
+    'functions-Spectrum.R'
+    'functions-Spectrum1.R'
+    'functions-Spectrum2.R'
+    'functions-addIdentificationData.R'
+    'functions-fragments.R'
+    'functions-mzR.R'
+    'functions-plotting.R'
+    'header.R'
+    'hmap.R'
+    'iPQF.R'
+    'iTRAQ4.R'
+    'iTRAQ5.R'
+    'iTRAQ8.R'
+    'iTRAQ9.R'
+    'imputation.R'
+    'map.R'
+    'matching.R'
+    'methods-Chromatogram.R'
+    'methods-Chromatograms.R'
+    'methods-MIAPE.R'
+    'methods-MSnExp.R'
+    'methods-MSnProcess.R'
+    'methods-MSnSet.R'
+    'methods-MSnSetList.R'
+    'methods-NAnnotatedDataFrame.R'
+    'methods-OnDiskMSnExp.R'
+    'methods-ProcessingStep.R'
+    'methods-ReporterIons.R'
+    'methods-Spectrum.R'
+    'methods-Spectrum1.R'
+    'methods-Spectrum2.R'
+    'methods-all.equal.R'
+    'methods-filters.R'
+    'methods-fragments.R'
+    'methods-mzR.R'
+    'methods-other.R'
+    'methods-pSet.R'
+    'methods-updateObjectTo.R'
+    'methods-write.R'
+    'missing-data.R'
+    'nadata.R'
+    'nav.R'
+    'options.R'
+    'plotting-MSnExp.R'
+    'plotting-MSnSet.R'
+    'plotting-OnDiskMSnExp.R'
+    'plotting-Spectrum.R'
+    'plotting-Spectrum1.R'
+    'plotting-Spectrum2.R'
+    'plotting-dataframe.R'
+    'quantitation-MS2-isobaric.R'
+    'quantitation-MS2-labelfree.R'
+    'readChromData.R'
+    'readMSData.R'
+    'readMSData2.R'
+    'readMSnSet.R'
+    'readMzXMLData.R'
+    'readWriteMgfData.R'
+    'readWriteMzTab.R'
+    'utils.R'
+    'writeMSData.R'
+    'zzz.R'

NAMESPACE

@@ -33,8 +33,9 @@ importFrom(ggplot2, geom_histogram, geom_text, geom_line, geom_point,
            facet_grid)
 
 importFrom(MALDIquant, binPeaks, match.closest) ## only using ::: functions
-importFrom(S4Vectors, isEmpty, metadata, DataFrame)
-importFrom(S4Vectors, isEmpty, metadata, DataFrame, replaceROWS)
+importFrom(S4Vectors, isEmpty, metadata, DataFrame, replaceROWS, SimpleList)
+importMethodsFrom(S4Vectors, showAsCell, "mcols<-", mcols, split)
+importClassesFrom(S4Vectors, SimpleList)
 importFrom(MASS, rlm)
 
 ## importFrom(rols, olsQuery, term)
@@ -149,7 +150,8 @@ export(MSnSet,
        combineSpectraMovingWindow,
        estimateMzScattering,
        hasSpectra, hasChromatograms,
-       mergeFeatureVars, expandFeatureVars
+       mergeFeatureVars, expandFeatureVars,
+       SpectrumList
        )
 
 exportClasses(pSet,
@@ -168,7 +170,9 @@ exportClasses(pSet,
               OnDiskMSnExp,
               ProcessingStep,
               Chromatogram,
-              Chromatograms)
+              Chromatograms,
+	      SpectrumList
+	      )
 
 exportMethods(updateObject,
               exprs,

NEWS

@@ -1,7 +1,7 @@
 # MSnbase 2.7
 
 Changes in version 2.7.8
-- Nothing yet
+- Add SpectrumList class
 
 Changes in version 2.7.7
 - Fix unit tests (issue #360, wrong MS OBO CV terms for data smoothing

NEWS.md

@@ -1,7 +1,7 @@
 # MSnbase 2.7
 
 ## Changes in version 2.7.8
-- Nothing yet
+- Add SpectrumList class.
 
 ## Changes in version 2.7.7
 - Fix unit tests (issue [#360](https://github.com/lgatto/MSnbase/issues/360), wrong MS OBO CV terms for data smoothing